scholarly journals Bacterial chromosomal mobility via lateral transduction exceeds that of classical mobile genetic elements

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Suzanne Humphrey ◽  
Alfred Fillol-Salom ◽  
Nuria Quiles-Puchalt ◽  
Rodrigo Ibarra-Chávez ◽  
Andreas F. Haag ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Horizontal Gene Transfer ◽  
Horizontal Transfer ◽  
Mobile Genetic Elements ◽  
Transfer Rates ◽  
High Frequencies ◽  
Genetic Elements ◽  
Chromosomal Genes ◽  
Definition Of ◽  
Generalized Transduction

AbstractIt is commonly assumed that the horizontal transfer of most bacterial chromosomal genes is limited, in contrast to the frequent transfer observed for typical mobile genetic elements. However, this view has been recently challenged by the discovery of lateral transduction in Staphylococcus aureus, where temperate phages can drive the transfer of large chromosomal regions at extremely high frequencies. Here, we analyse previously published as well as new datasets to compare horizontal gene transfer rates mediated by different mechanisms in S. aureus and Salmonella enterica. We find that the horizontal transfer of core chromosomal genes via lateral transduction can be more efficient than the transfer of classical mobile genetic elements via conjugation or generalized transduction. These results raise questions about our definition of mobile genetic elements, and the potential roles played by lateral transduction in bacterial evolution.

scholarly journals Role of Horizontal Gene Transfer in the Development of Multidrug Resistance in Haemophilus influenzae

mSphere ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Kristin Hegstad ◽  
Haima Mylvaganam ◽  
Jessin Janice ◽  
Ellen Josefsen ◽  
Audun Sivertsen ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Haemophilus Influenzae ◽  
Resistance Genes ◽  
Mobile Genetic Elements ◽  
Beta Lactam ◽  
Content Type ◽  
Genetic Elements ◽  
Wide Range ◽  
Chromosomal Genes

ABSTRACT Haemophilus influenzae colonizes the respiratory tract in humans and causes both invasive and noninvasive infections. Resistance to extended-spectrum cephalosporins in H. influenzae is rare in Europe. In this study, we defined acquired resistance gene loci and ftsI mutations in multidrug-resistant (MDR) and/or PBP3-mediated beta-lactam-resistant (rPBP3) H. influenzae strains, intending to understand the mode of spread of antibiotic resistance determinants in this species. Horizontal transfer of mobile genetic elements and transformation with resistance-conferring ftsI alleles were contributory. We found one small plasmid and three novel integrative conjugative elements (ICEs) which carry different combinations of resistance genes. Demonstration of transfer and/or ICE circular forms showed that the ICEs are functional. Two extensively MDR genetically unrelated H. influenzae strains (F and G) from the same geographical region shared an identical novel MDR ICE (Tn6686) harboring blaTEM-1, catA2-like, and tet(B). The first Nordic case of MDR H. influenzae septicemia, strain 0, originating from the same geographical area as these strains, had a similar resistance pattern but contained another ICE [Tn6687 with blaTEM-1, catP and tet(B)] with an overall structure quite similar to that of Tn6686. Comparison of the complete ftsI genes among rPBP3 strains revealed that the entire gene or certain regions of it are identical in genetically unrelated strains, indicating horizontal gene transfer. Our findings illustrate that H. influenzae is capable of acquiring resistance against a wide range of commonly used antibiotics through horizontal gene transfer, in terms of conjugative transfer of ICEs and transformation of chromosomal genes. IMPORTANCE Haemophilus influenzae colonizes the respiratory tract in humans and causes both invasive and noninvasive infections. As a threat to treatment, resistance against critically important antibiotics is on the rise in H. influenzae. Identifying mechanisms for horizontal acquisition of resistance genes is important to understand how multidrug resistance develops. The present study explores the antimicrobial resistance genes and their context in beta-lactam-resistant H. influenzae with coresistance to up to four non-beta-lactam groups. The results reveal that this organism is capable of acquiring resistance to a wide range of commonly used antibiotics through conjugative transfer of mobile genetic elements and transformation of chromosomal genes, resulting in mosaic genes with a broader resistance spectrum. Strains with chromosomally mediated resistance to extended-spectrum cephalosporins, co-trimoxazole, and quinolones combined with mobile genetic elements carrying genes mediating resistance to ampicillin, tetracyclines, and chloramphenicol have been reported, and further dissemination of such strains represents a particular concern.

scholarly journals A mobile genetic element increases bacterial host fitness by manipulating development

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Joshua M Jones ◽  
Ilana Grinberg ◽  
Avigdor Eldar ◽  
Alan D Grossman
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Mobile Genetic Elements ◽  
Selective Advantage ◽  
Host Cells ◽  
Bacterial Host ◽  
Host Fitness ◽  
Genetic Elements ◽  
Necessary And Sufficient ◽  
Integrative And Conjugative Element

Horizontal gene transfer is a major force in bacterial evolution. Mobile genetic elements are responsible for much of horizontal gene transfer and also carry beneficial cargo genes. Uncovering strategies used by mobile genetic elements to benefit host cells is crucial for understanding their stability and spread in populations. We describe a benefit that ICEBs1, an integrative and conjugative element of Bacillus subtilis, provides to its host cells. Activation of ICEBs1 conferred a frequency-dependent selective advantage to host cells during two different developmental processes: biofilm formation and sporulation. These benefits were due to inhibition of biofilm-associated gene expression and delayed sporulation by ICEBs1-containing cells, enabling them to exploit their neighbors and grow more prior to development. A single ICEBs1 gene, devI (formerly ydcO), was both necessary and sufficient for inhibition of development. Manipulation of host developmental programs allows ICEBs1 to increase host fitness, thereby increasing propagation of the element.

scholarly journals Host range and genetic plasticity explain the co-existence of integrative and extrachromosomal mobile genetic elements

2018 ◽  
Author(s):  
Jean Cury ◽  
Pedro H. Oliveira ◽  
Fernando de la Cruz ◽  
Eduardo P.C. Rocha
Keyword(s):  
Antibiotic Resistance ◽  
Horizontal Gene Transfer ◽  
Host Range ◽  
Antibiotic Resistance Genes ◽  
Mobile Genetic Elements ◽  
The Other ◽  
Microbial Populations ◽  
Dna Repeats ◽  
Genetic Elements ◽  
Integrative And Conjugative Elements

AbstractSelf-transmissible mobile genetic elements drive horizontal gene transfer between prokaryotes. Some of these elements integrate in the chromosome, whereas others replicate autonomously as plasmids. Recent works showed the existence of few differences, and occasional interconversion, between the two types of elements. Here, we enquired on why evolutionary processes have maintained the two types of mobile genetic elements by comparing integrative and conjugative elements (ICE) with extrachromosomal ones (conjugative plasmids) of the highly abundant MPFT conjugative type. We observed that plasmids encode more replicases, partition systems, and antibiotic resistance genes, whereas ICEs encode more integrases and metabolism-associated genes. ICEs and plasmids have similar average sizes, but plasmids are much more variable, have more DNA repeats, and exchange genes more frequently. On the other hand, we found that ICEs are more frequently transferred between distant taxa. We propose a model where differential plasticity and transmissibility range explain the co-occurrence of integrative and extra-chromosomal elements in microbial populations. In particular, the conversion from ICE to plasmid allows ICE to be more plastic, while the conversion from plasmid to ICE allows the expansion of the element‘s host range.

scholarly journals Disentangling the effects of selection and loss bias on gene dynamics

2017 ◽  
Author(s):  
Jaime Iranzo ◽  
José A. Cuesta ◽  
Susanna Manrubia ◽  
Mikhail I. Katsnelson ◽  
Eugene V. Koonin
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Genome Size ◽  
Mobile Genetic Elements ◽  
Loss Ratio ◽  
Effective Population ◽  
Strong Selection ◽  
Genetic Elements ◽  
Defense Systems ◽  
Parasite Defense

ABSTRACTWe combine mathematical modelling of genome evolution with comparative analysis of prokaryotic genomes to estimate the relative contributions of selection and intrinsic loss bias to the evolution of different functional classes of genes and mobile genetic elements (MGE). An exact solution for the dynamics of gene family size was obtained under a linear duplication-transfer-loss model with selection. With the exception of genes involved in information processing, particularly translation, which are maintained by strong selection, the average selection coefficient for most non-parasitic genes is low albeit positive, compatible with the observed positive correlation between genome size and effective population size. Free-living microbes evolve under stronger selection for gene retention than parasites. Different classes of MGE show a broad range of fitness effects, from the nearly neutral transposons to prophages, which are actively eliminated by selection. Genes involved in anti-parasite defense, on average, incur a fitness cost to the host that is at least as high as the cost of plasmids. This cost is probably due to the adverse effects of autoimmunity and curtailment of horizontal gene transfer caused by the defense systems and selfish behavior of some of these systems, such as toxin-antitoxin and restriction-modification modules. Transposons follow a biphasic dynamics, with bursts of gene proliferation followed by decay in the copy number that is quantitatively captured by the model. The horizontal gene transfer to loss ratio, but not the duplication to loss ratio, correlates with genome size, potentially explaining the increased abundance of neutral and costly elements in larger genomes.SIGNIFICANCEEvolution of microbes is dominated by horizontal gene transfer and the incessant host-parasite arms race that promotes the evolution of diverse anti-parasite defense systems. The evolutionary factors governing these processes are complex and difficult to disentangle but the rapidly growing genome databases provide ample material for testing evolutionary models. Rigorous mathematical modeling of evolutionary processes, combined with computer simulation and comparative genomics, allowed us to elucidate the evolutionary regimes of different classes of microbial genes. Only genes involved in key informational and metabolic pathways are subject to strong selection whereas most of the others are effectively neutral or even burdensome. Mobile genetic elements and defense systems are costly, supporting the understanding that their evolution is governed by the same factors.

scholarly journals CRISPR-Cas Loci of Yersinia pseudotuberculosis Strains with Different Genetic Determinants

2020 ◽  
Vol 19 (2) ◽  
pp. 31-39
Author(s):  
N. P. Peretolchina ◽  
V. T. Klimov ◽  
E. A. Voskresenskaya ◽  
G. I. Kokorina ◽  
E. A. Bogumilchik ◽  
...  
Keyword(s):  
Clinical Manifestation ◽  
Horizontal Transfer ◽  
Yersinia Pseudotuberculosis ◽  
Mobile Genetic Elements ◽  
Severe Form ◽  
Virulence Determinants ◽  
Genetic Determinants ◽  
Genetic Elements ◽  
Serotype O ◽  
Specific Virulence

Relevance. Yersinia pseudotuberculosis is a causative agent of pseudotuberculosis, a disease with polymorphism of clinical manifestation that is determined by the presence of specific virulence determinants: plasmid pVM82, pathogenicity islands HPI and YAPI, and superantigen YPM. Occurrence of new determinants depends on horizontal transfer of mobile genetic elements, hence, systems regulating horizontal transfer participate in evolution of pathogenic species. CRISPR-Cas is and adaptive protection system of prokaryotes against mobile genetic elements. Aim. The study analyzed an interaction between CRISPR-loci of Y. pseudotuberculosis and virulence determinants. Results. 86% of strains includes three CRISPR-loci: YP1, YP2, and YP3. Length of locus YP3 mostly depends on presence of virulence determinants in strains of Y. pseudotuberculosis serotype O:1b. Strains with virulence genes are able to cause a severe form of pseudotuberculosis and have longer locus than strains without determinants. Conclusion. Therefore, CRIPSRCas system of Y. pseudotuberculosis may participate in formation of a certain strain genotype that defines clinical manifestation of pseudotuberculosis.

scholarly journals Non-canonical Staphylococcus aureus pathogenicity island repression

2021 ◽  
Author(s):  
Laura Miguel-Romero ◽  
Mohammed Alqasmi ◽  
Julio Bacarizo ◽  
Jason A. Tan ◽  
Richard J. Cogdell ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Dna Binding ◽  
Virulence Factors ◽  
Pathogenicity Island ◽  
Mobile Genetic Elements ◽  
Life Cycles ◽  
Genetic Elements ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Induction System

ABSTRACTMobile genetic elements (MGEs) control their life cycles by the expression of a master repressor, whose function must be disabled to allow the spread of these elements in nature. Here we describe an unprecedented repression-derepression mechanism involved in the transfer of the Staphylococcus aureus pathogenicity islands (SaPIs). Contrary to the classical phage and SaPI repressors, which are dimers, the SaPI1 repressor StlSaPI1 presents a unique tetrameric conformation, never seen before. Importantly, not just one but two tetramers are required for SaPI1 repression, which increases the novelty of the system. To derepress SaPI1, the phage-encoded protein Sri binds to and induces a conformational change in the DNA binding domains of StlSaPI1, preventing the binding of the repressor to its cognate StlSaPI1 sites. Finally, our findings demonstrate that this system is not exclusive to SaPI1 but widespread in nature. Overall, our results characterise a novel repression-induction system involved in the transfer of MGE-encoded virulence factors in nature.SignificanceWhile most repressors controlling the transfer of mobile genetic elements are dimers, we demonstrate here that the Staphylococcal pathogenicity island 1 (SaPI1) is repressed by two tetramers, which have a novel structural fold in their body that has never been seen before in other proteins. Moreover, by solving the structure of the SaPI1 repressor in complex with its inducing protein Sri, we have demonstrated that Sri forces the SaPI1 repressor to adopt a conformation that is incompatible with DNA binding, explaining how SaPI1 is induced. Finally, our results demonstrate that this repression system is not exclusive of the SaPIs but widespread in nature. Our studies provide important insights understanding how SaPIs spread in nature.

scholarly journals In situ detection of horizontal transfer of mobile genetic elements

2002 ◽  
Vol 42 (2) ◽  
pp. 261-268 ◽  
Author(s):  
Janus A.J. Haagensen ◽  
S.K. Hansen ◽  
T. Johansen ◽  
S. Molin
Keyword(s):  
Horizontal Transfer ◽  
Mobile Genetic Elements ◽  
Genetic Elements ◽  
In Situ Detection

scholarly journals Draft Genome Sequences of 14 Staphylococcus aureus Sequence Type 5 Isolates from California, USA

2017 ◽  
Vol 5 (13) ◽  
Author(s):  
Samantha J. Hau ◽  
Darrell O. Bayles ◽  
David P. Alt ◽  
Tracy L. Nicholson
Keyword(s):  
Staphylococcus Aureus ◽  
Draft Genome ◽  
Mobile Genetic Elements ◽  
Sequence Type ◽  
Genome Sequences ◽  
Content Type ◽  
Genetic Elements

ABSTRACT Staphylococcus aureus is part of the human epithelial microbiota; however, it is also a pathogen. The acquisition of mobile genetic elements plays a role in the virulence of S. aureus isolates and contributes to treatment failures. This report details the draft genome sequences of 14 clinical S. aureus isolates.

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